Goodman's first appointment was to the rectory of Stapleford Abbotts, Essex, in 1606. He made rapid progress in the Church, and was made successively prebend of Westminster in 1607; Rector of West Isley, Berkshire, in 1616; Rector of Kinnerton, Gloucester; Canon of Windsor in 1617; Dean of Rochester in 1620-1621; and finally Bishop of Gloucester, 1624-1655. In addition, he held two livings in Wales, at Llandyssil and Llanarmon. Even as a bishop, he was allowed to retain most of these appointments.
It is likely that doubts were arising in his mind about the legitimacy of the Church's separation from Rome, and he sought the society of Catholic priests who were in hiding throughout the country. He was frequently at variance with Archbishop Laud, and in 1640 refused on conscientious grounds to sign the seventeen Articles drawn up by the Archbishop. He was thereupon arrested, but after five weeks in prison he overcame his scruples and signed the Articles. This, however, availed him little, as he was soon impeached by Parliament along with Laud and the ten other signatories of the Articles and was sent to prison for four months.
In 1643, Goodman's episcopal palace was pillaged by parliamentarian soldiers and over the course of a couple of years he was stripped of all his emoluments. He withdrew from public life to his small Welsh estate in Carnarvon, and it is likely that he converted to Catholicism at this time.
In about 1650, he came to London, and gave himself up to study and research; he was befriended by some Catholic royalists and lived in close connection with them until his death in 1656. Father Davenport, O.S.F., former chaplain to Queen Henrietta, was his confessor and attended him in his last illness. By his will, in which he made a profession of his Catholic faith, he left most of his property to Ruthin, his native town; his manuscripts and books, however, were given to Trinity College, Cambridge.